modelling potential current distribution and future
TRANSCRIPT
BIODIVERSITAS ISSN: 1412-033X Volume 21, Number 2, February 2020 E-ISSN: 2085-4722 Pages: 674-682 DOI: 10.13057/biodiv/d210233
Modelling potential current distribution and future dispersal of an
invasive species Calliandra calothyrsus in Bali Island, Indonesia
ANGGA YUDAPUTRA
Center of Plant Conservation and Botanic Gardens, Indonesian Institute of Sciences. Jl. Ir. H. Djuanda No.13, Paledang, Bogor 16211, West Java,
Indonesia. Tel./fax.: +62-251-8311362-8336871, email: [email protected]
Manuscript received: 1 November 2019. Revision accepted: 21 January 2020.
Keywords: Calliandra calothyrsus, invasive plant, population structure, population dispersal, species distribution model
INTRODUCTION
Calliandra calothyrsus Meisn. is a small tree or large
shrub belong to Fabaceae family (Macqueen 1992). It
normally reaches 6 m high, but can be up to 12 m under
favorable conditions. The stem is relatively small with
maximum diameter at the base about 30 cm, and the bark is
blackish-brown. The flower of the plant has many long red
stamens with the flowering phase starts from 3-6 months
after planting. The fruits have many pods that contain 3-12
seeds and the seeds will mature about 3 months after
pollination. The root relatively grows deep and has long-lived sprouts up to 20 years (Ad Hoc Panel 1983). C.
calothyrsus has a relatively rapid growth at early stage. It
often outcompetes other plants at later stage and invades
abandoned lands such as roadsides or shifting cultivation
fields. It is well adapted at wide range of altitudes, from sea
level to 1,860 m in area with annual precipitation ranges
from 700 to 3,000 mm (Lowry and Macklin 1989). It grows
well on wide range of soil types from deep volcanic loams
to sandy clay (Galang 1988). It occupies area with the
range of mean monthly maximum temperatures between 24
and 28°C and means minimum temperatures of 18-24°C
(Wiersum and Rika 1992). Calliandra calothyrsus is native to humid and sub-
humid regions of Central America to Mexico. In 1936, this
plant was introduced from Guatemala to Java. Recently, the
plant is easily found throughout the Indonesian archipelago
and in other parts of Southeast Asia. It was widely utilized
as source of green manure and shade for coffee plantation
at that time (Verhoef 1939). During the 1970s, it was
massively planted in many areas in Java and other regions
of Indonesia sponsored by the Indonesian State Forest
Corporation (Perum Perhutani). The program was intended
to achieve the term of a true self-perpetuating greening
movement (Palmer et al. 1994). Many benefits of this plant
have been generated since the first year of introduction in
Java. Local people have been used the stem as firewood,
the young foliage to feed livestock, and the nectar for
producing bees honey (Hauser et al. 2006). It is considered a pioneer plant because it can grow in poor soil conditions
with limited nutrient availability. It adapts easily to various
soil types and is tolerant to wide range of environmental
factors such as altitude, rainfall, and light intensity. Further-
more, it is potentially used to fix nitrogen from atmosphere
and improve soil fertility and stability (Ad Hoc Panel 1983).
It tends to be more adaptive in extreme conditions (e.g. lack
of nutrients, poor soil quality and abandoned land) as well
as has highly reproduction ability and wide seed dispersal.
It was considered an invasive plant in several regions. It
was recently invading Karibia, Hawai, Uganda, Dominican
Republic, and Indonesia (Kairo et al. 2003; Orwa et al. 2009; Setyawati et al. 2015). It was widely introduced to
the tropic and sub-tropic region and recorded as an invasive
plant based on Invasive Species Compendium (CABI
2017). According to these reasons, this plant is often
considered as invasive species that can negatively impact
biodiversity by displacing native species.
Abstract. Yudaputra A. 2020. Modelling potential current distribution and future dispersal of an invasive species Calliandra calothyrsus in Bali Island, Indonesia. Biodiversitas 21: 674-682. Calliandra calothyrsus Meisn. is relatively well-adapted in abandoned areas, degraded lands, and poor nutrient soils. It tends to reproduce rapidly and be invasive in certain landscapes as it often dominates the vegetation. This study aimed to understand the potential current distribution and the population dispersal of C. calothyrsus across Bali Island using Random Forest (RF) and Maximum Entropy (MaxEnt) models. Thirteen environmental variables, including several climatic variables, topography, soil characteristics were used as predictors. The occurrence records of C. calothyrsus were obtained from direct field survey in which square plots 10 x 10 m were used to collect the population structure data. The Rangeshifter software was used to understand the population dynamic and dispersal pattern. The results showed that the two models (RF and MaxEnt) have the AUC>0.9 which means those models are excellent in predicting the potential current distribution of C. calothyrsus. Furthermore, the RF model has the TSS and Kappa value of >0.90 which means it has almost perfect agreement between the prediction and the real observation. On the other hand, the TSS and Kappa value of MaxEnt were >0.70 indicating it has a substantial agreement. The population structure in the field showed that the number of juvenile individuals dominated all plots compared to seedlings and mature individuals. The simulation analysis showed that the population tends to have bigger population in the next 50 years by dispersing throughout neighbor cells or areas in which the origin occurrence points were recorded.
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Figure 1. The morphology of Calliandra calothyrsus
Invasive species are defined as non-native or alien
species that occupy and dominates particular landscape or
ecosystem. Invasive plants are more likely to be successful
to establish and spread in a landscape because many
invasive plants are able to produce seeds in high quantities
which are easily dispersed by wind or birds. They can adapt to disturbed soil or abandoned land with poor soil
nutrients. Some invasive plants have aggressive root
systems that rapidly grow over large areas, some of them
produce chemical substances that inhibit other organisms to
live in its surrounding. The invasion of alien species in an
environment causes many problems, such as threatening
native species moreover the threatened and endangered
species, increasing the risk of soil erosion, and contributing
to the poor quality of agricultural lands (USDA 2019). For
landscape management purposes, understanding the
potential invasion of C. calothyrsus will be necessary as a consideration regarding proper management control. With
fairly rapid population growth, it needs to be monitored for
its development in the future. In terms of understanding the
distribution and dispersal of invasive alien species, the use
of species distribution modelling might be useful for
providing information regarding the mitigation and
management strategies. Predictive models of species
geographic distribution have been used in ecology and
conservation (Graham et al. 2004). There are many
application of species distribution modelling in ecology,
such as modelling the impact of climate change to species distribution (Thomas et al. 2004), modelling the spread
pattern of invasive species (Thuiller et al. 2005), and the
spatial pattern of species diversity (Graham et al. 2006).
Recently, many species distribution models have been
developed to understand the pattern of biodiversity
distribution.
Random forest (RF) is a machine learning that works based on regression and classification tree (Breiman 2001;
Liaw and Wiener 2002). RF is widely used in ecology
because it performs better as a classifier
(Cutler et al. 2007). Random Forest is a robust predictive
model that often used when the number of data points is
smaller compared to environmental predictors (Strobl
et al. 2007). RF outperforms than other species distribution
models (e.g. GLM, GAM, MARS, ANN) (Yudaputra et al.
2019). Furthermore, RF outperforms other predictive
models in predicting the distribution of Eusideroxylon
zwageri in Kalimantan (Yudaputra et al. 2020). Maximum Entropy (MaxEnt) is a modelling technique that can
achieve high predictive accuracy (Phillips and Dudik
2008). There are several advantages using MaxEnt, such as
it works both continuous and categorical data, it possibly
runs with presence only data, and overfitting can be
avoided (Phillips et al, 2006). In recent study, MaxEnt
shows the highest Area Under the Curve (AUC) value
compared to other species distribution models (e.g. RF,
SVM, GLM, BIOCLIM, DOMAIN) in predicting of
Guettarda speciosa (Yudaputra et al. 2019).
Area Under the Curve values (AUC) of receiver operator characteristic (ROC) curves, True Skill Statistics
BIODIVERSITAS 21 (2): 674-682, February 2020
676
(TSS), and Kappa statistic are used to measure the accuracy
of predictive models. The AUC is often used as a standard
to measure the accuracy of species distribution model
(Fielding and Bell 1997; Lobo et al. 2008). When the AUC
value > 0.5, it indicates the model works better than
random chance (Krzanowski and Hand 2009). The AUC
value represents how better model performance in which it
can be divided into several categories, i.e. 0.9-1 (excellent),
0.8-0.9 (good), 0.7-0.8 (fair), 0.6-0.7 (poor), and 0.5-0.6
(fail) (Krzanowski and Hand 2009). TSS is often used to evaluate the performance of model prediction and referred
to as Pierce skill score (Stephenson 2000). The TSS has the
range from-1 to +1 in which the value of +1 indicates
perfect agreement and value of zero or less indicates the
performance no better than random chance. The value of
TSS is categorized as follows, < 0.4 were poor, 0.4-0.8
useful, and > 0.8 good to excellent (Allouche et al. 2006).
Kappa represents the agreement between two binary
variables. Kappa is a measurement that also used in species
distribution modelling. The score of Kappa can be defined
as follows, 0 = agreement equivalent to chance, 0.1-0.20 = slight agreement, 0.21-0.40 = fair agreement, 0.41-0.60 =
moderate agreement, 0.61-0.80 = substantial agreement,
0.81-0.99 = near perfect agreement, 1 = perfect agreement
(Stephanie 2014).
Plant population dynamic refers to how the populations
change in their number through space and time by
quantifying their births, deaths, immigration, and
emigrations. The populations tend to exponentially increase
when they occupy in suitable conditions with freely
available resources. There are several factors that
determine the dynamic of population including demography, weather, soil condition, competitors,
herbivore, pathogen, and various hazards (fire) (Watkinson
1997). In case to understand the population growth and
dynamic, the use of matrices is strongly recommended. The
matrices in ecology that have been widely well known to
understand the population growth is Leslie matrix. It was
used to model the change of organisms in population over
period of time. The Leslie matrix works by dividing
population into several groups based on the age classes
(Caswell 2001). By combining the spatial analysis and
population demography, we could understand how the
population disperses in landscape. In study of invasive species, incorporating the correlative model and
mechanistic model would produce a useful predictive
model (Yudaputra 2019).
MATERIALS AND METHODS
Modelling potential current distribution
The current climatic variables were obtained from the
global climate data of the new version 2.0. Eight climatic
variables were chosen in this study: BIO1 = Annual Mean
Temperature, BIO4 = Temperature Seasonality (standard
deviation *100), BIO5 = Max Temperature of Warmest
Month, BIO6 = Min Temperature of Coldest Month, BIO12 = Annual Precipitation, BIO13 = Precipitation of
Wettest Month, BIO14 = Precipitation of Driest Month,
BIO15 = Precipitation Seasonality (Coefficient of
Variation). Those climatic data were available on raster
format (tiff) for all regions across the globe. The climatic
data are extracted from the global climatic data
(worldclim.org). The resolution 900 m (30 arc-second
resolution) was chosen for all climatic variables. Physical
environment variables were also used as a predictor in this
model. Those were elevation, soil pH, soil type, land cover,
and evapotranspiration. The topographic data are obtained
from the global data (earthexplorer.usgs.gov) and the soil data are extracted from soil grid global data (soilgrids.org).
Those variables were chosen because those are suspected
as physical environments that determining the distribution
pattern of this species. Both climatic and environmental
variables should have the same resolution that required to
run the species distribution modelling. The variables which
have finer resolution were downgraded as the other
variables. All spatial data in raster format (tiff) were
clipped to align with the study area (Bali). Those clipped-
climatic variables and physical environment variables were
then used for modelling process in R open sources. Two algorithms of species distribution model were used
to model potential current and future distribution of C.
calothyrsus. Those algorithms were Random Forest (RF)
and Maximum Entropy (MaxEnt). Several R packages
were used in this modelling such as “dismo” was used to
load climate variables, “randomforest” was used to run
Random Forest model, “rJava” was used to run the MaxEnt
model, “mapview” was used to see the point of
occurrences, library “sdm” was used to run several
algorithms of species distribution models. All algorithms
were run using “bootstrap” with two replications.
Field assessment of population structure
The population of Calliandra calothyrsus at secondary
forest in Pinggan village, Bangli District was used to
understand the population dynamic pattern. The population
of C. calothyrsus was grouped into several classes based on
its growth stage. Seedling individuals (0-2 m), juvenile
individuals (2-12 m), mature (individuals that entering the
flowering or fruiting phase). Ten plots with size 10 x 10 m
were established to record the individuals and group them
into several classes of growth stage. RANGESHIFTER
Ver.1.0 software was used to understand the population
dynamics of the species for 40 years.
Modelling population dispersal
Land use map of Indonesia was used to provide the
landscape feature in this model. The map consists of 17
types of land uses and covers all regions of Indonesia. The
polygon of the land use map was clipped with the base map
of Bali to extract only land-use of Bali. Then, the original
land use data projection (i.e. WGS 84) was converted into
UTM (Universal Transverse Mercator) coordinate
projection. The conversion of coordinate system is needed
because the RANGESHIFTER 1.0 requires inputs with
UTM projections. Then, the land use data as a polygon with UTM projection was converted into raster format. We
used 500 m resolution in spatial data preparation as inputs.
The last steps of spatial data preparation were converting
YUDAPUTRA et al. – Potential distribution of Calliandra calothyrsus in Bali Island, Indonesia
677
format of data from into asci as required in
RANGESHIFTER Software.
Point of occurrence data in XLXS or CSV (Comma
Delimited) format was loaded into GIS with the coordinate
projection was adjusted to UTM. The data was then
converted into shapefile (shp) of point occurrence. The
shapefile was converted into raster file format with a
resolution of 500 m. The last step, raster data was changed
into asci format as required in RANNGESHIFTER ver.1.0
software. Land use and point of occurrence should have the same coordinate projection and resolution as inputs of
software.
In RANGESHIFTER, the population dynamic data
should be fitted with several population parameters. The
Leslie matrix population would be helpful to understand
the population class. The probabilities of seedlings grow to
juvenile (G1 stage), the probabilities juvenile grow to
mature individual (G2 stage), the fecundity of mature
individual, the age required by mature individuals to
produce their offspring, and density dependence. We set
the probability of growing phase from seedling to juvenile as 0.6 and the probability of growing from juvenile to
mature individual as 0.3 in which both values were derived
from calculations. The minimum age of mature individuals
to reproduce offspring was approximately 5 years. The
survival probability was set to 0.8, and the fecundity of
mature individual was 90. The density independence was
set to 0.1 and mortality probability was 0.2. If the arrival
cells were unsuitable, the models will randomly choose a
suitable neighbor cell/grid. Mean distance of 500 m was
used in this dispersal model. The simulation was run for 2
replications. Two hundred individuals per cell were inputted in this model and the proportion of individuals per
stage 1 : stage 2 = 0.6 : 0.4. The simulation was run for 50
years to understand the dynamics of C. calothyrsus
population across the Bali landscape. The predictive
dynamic population maps were created every 10 years
throughout 50 years of simulation.
RESULTS AND DISCUSSION
Results
Two algorithms of species distribution models were
used to predict the potential current distribution of
Calliandra calothyrsus. In this study, three parameters of
model evaluation were used to evaluate model performance. Those were AUC value, True Skill Statistics
(TSS), and Kappa statistic. The AUC value of RF (0.98)
was better than that of MaxEnt (0.92) (Table 1). The two
models have the AUC value >0.90, indicating excellent
model performance in predicting the potential current
distribution. The TSS value of RF was much higher than
that of MaxEnt with 0.90 and 0.72 respectively. The TSS
value of RF >0.90 indicating that the performance of model
was excellent. On the other hands, the TSS value of
MaxEnt >0.70 indicating the model performance was good.
The last evaluation parameters used in this model were Kappa. The Kappa value of RF was 0.95 which means it
has almost perfect agreement between prediction and real
observation. Meanwhile, the Kappa value of MaxEnt was
0.79 indicating the model has substantial agreement. RF
predicted most accurately three predictors that determine
distribution patterns, which were elevation,
evapotranspiration, and precipitation (Figure 3).
Meanwhile, MaxEnt produced three most important
predictors including elevation, temperature, and
precipitation (Figure 4). The two models produced almost
similar predictive maps of potential current distribution of C. calothyrsus (Figures 5 and 6).
The results of our field survey showed that mature
individuals were relatively small in number compared to
seedlings and juvenile individuals in which only 3-5 mature
individuals were found at each plot. The juvenile
individuals were the most dominant in every plot. In
population structure analysis, the total of mature
individuals was 44, juvenile individuals 354, and seedlings
109 (Figure 7). Our simulation analysis indicated that
population tends to increase rapidly over 50 years of
simulation by dispersing in neighboring cells or locations. The population continuously growing for every ten years of
simulation.
Discussion
Species Distribution Models (SDMs) were often used to
understand the potential distribution area of a species by
incorporating physical environment variables and presence
only records or presence-absence records. In this study,
thirteen environmental variables were used to run this
model because those variables were presumably important
in terms of determining the distribution pattern. The
selection of environmental variables should consider the presence requirement of the species. The selection of
environmental variables was a critical way of determining
the accuracy of predictive model. In model calibration,
dataset was divided into training and testing data in which
training data was used for developing the model, whereas
the testing data was used for evaluating the model
performance. The testing data for evaluation was ideally
obtained from resampling which was considered as
independent data. However, splitting data was often
considered as the best solution since the time and effort to
resample the data were limited. In our analysis, we used the
proportion of training data: testing data = 75 : 25. Based on the results of this study, according to three parameters of
evaluation (i.e. AUC, TSS, Kappa), the predictive models
produced by RF and MaxEnt were categorized as excellent
predictive models. Those models were highly
recommended to be used in prediction of potential
distribution. Table 1. The evaluation of model performance using the AUC, TSS, and Kappa
Methods AUC TSS Kappa
Random Forest (RF) 0.98 0.90 0.95 Maximum Entrophy (MaxEnt) 0.92 0.72 0.79
BIODIVERSITAS 21 (2): 674-682, February 2020
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Figure 2. The ROC and AUC value: A. Random Forest (RF); B. Maximum Entropy (MaxEnt)
Figure 3. The relative importance of environment variables using Random Forest (RF)
Figure 4. The relative importance of environmental variables using Maximum Entropy (MaxEnt)
YUDAPUTRA et al. – Potential distribution of Calliandra calothyrsus in Bali Island, Indonesia
679
Figure 5. The predictive map of potential current distribution of Calliandra calothyrsus using Random Forest (RF)
Figure 6. The predictive map of potential current distribution of Calliandra calothyrsus using MaxEnt
A B C
Figure 7. The population structure of Calliandra calothyrsus: A. Seedlings, B. Juvenile individuals, C. Mature individuals
140
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1
2
3
Year_20 Year_30
Year_40
Year_0
Year_50
Year_10
Figure 9. The population dispersal of Calliandra calothyrsus across Bali landscape. The orange color presents the growth of population of Calliandra calothyrsus throughout 50 years simulation
Figure 10. Population dynamic of Calliandra calothyrsus throughout 50 years of simulation
Random Forest (RF) and Maximum Entropy (MaxEnt)
were chosen because those models outperform to other
SDMs models. MaxEnt produced the highest AUC value,
followed by SVM and RF in predicting of Zebra Wood
distribution (Yudaputra et al. 2019). Both two predictive
models (RF and MaxEnt) produced almost similar
YUDAPUTRA et al. – Potential distribution of Calliandra calothyrsus in Bali Island, Indonesia
681
environmental variables that are the most important in
terms of determining the distribution of this species. Those
were elevation, precipitation, and temperature. The
predictive maps will choose the regions across the
landscape that have similar physical environments in which
the species presence. According to the predictive map
produced from RF and MaxEnt, the potential current
distribution of Calliandra calothyrsus stretched from
Kintamani, Bedugul, Bangli, Ubud, and small part of
Gianyar and Klungkung. It mostly grew in abandoned, bare and shrublands. It seemed to well adapt in all elevation
gradients from lowland to upland, but mostly in lowland.
The predictive maps of potential invasion area would be
useful as a consideration for management control of this
species. Growing the native plants in area that predicted as
a suitable habitat for C. calothyrsus would be the best
strategies to prevent its invasiveness. When the invasive C.
calothyrsus has been invaded and dominated in landscape,
removing by cutting it down would be an alternative
solution for management control.
The population structure consisted of three different classes including seedlings, juveniles, and mature
individuals. According to population structure analysis
(Figure 7), the juvenile individuals were the most abundant
than other growth stages at all sampling plots. The juvenile
individuals have height from 6 to 12 m. At the sampling
plots, the juvenile individuals of C. calothyrsus dominated
other vegetation in their surroundings. Seedlings were
relatively found in few numbers. The mature individuals
were found with a height around 12-14 m which had many
pods containing mature seeds. The number of mature
individuals was 3-5 at each sampling plot. In the population dynamic modelling, the size of individuals is significantly
increased per 10 years of simulation. This might have
happened because the mature individuals were able to
produce many seeds in their reproduction phase. The seeds
produced by mature individuals are approximately up to
500 seeds. The number of individuals increases rapidly.
Rangeshifter was a novel dynamic modelling platform used
to understand the ecological and evolutionary communities
(Huntley et al. 2010; Morales et al. 2010; Schurr et al.
2012; Thuiller et al. 2013). It provides a modelling of
population dynamic and dispersal behaviors on landscape
at different scale. The populations seem to be rapidly increased throughout 50 years of simulation because the
plants will be able to produce seeds in high quantity. The
dispersal pattern started from the initial occurrence and
dispersed to neighboring cells. They tended to disperse in
area where the condition is suitable with supporting
resources available.
In conclusion, Random Forest (RF) and MaxEnt are
categorized as excellent predictive models that presented
with AUC value. Both two SDMs are relevant to predict
the distribution pattern of Calliandra calothyrsus. The
population of C. calothyrsus tends to have bigger number throughout 50-year simulation and disperses to the adjacent
locations on landscape.
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